GPU acceleration of time-domain fluorescence lifetime imaging

Fluorescence lifetime imaging microscopy (FLIM) plays a significant role in biological sciences, chemistry, and medical research. We propose a Graphic Processing Units (GPUs) based FLIM analysis tool suitable for high-speed and flexible time-domain FLIM applications. With a large number of parallel processors, GPUs can significantly speed up lifetime calculations compared to CPU-OpenMP (parallel computing with multiple CPU cores) based analysis. We demonstrate how to implement and optimize FLIM algorithms on GPUs for both iterative and non-iterative FLIM analysis algorithms. The implemented algorithms have been tested on both synthesized and experimental FLIM data. The results show that at the same precision the GPU analysis can be up to 24-fold faster than its CPU-OpenMP counterpart. This means that even for high precision but time-consuming iterative FLIM algorithms, GPUs enable fast or even real-time analysis

Empowering parallel computing with field programmable gate arrays

After more than 30 years, reconfigurable computing has grown from a concept to a mature field of science and technology. The cornerstone of this evolution is the field programmable gate array, a building block enabling the configuration of a custom hardware architecture. The departure from static von Neumannlike architectures opens the way to eliminate the instruction overhead and to optimize the execution speed and power consumption. FPGAs now live in a growing ecosystem of development tools, enabling software programmers to map algorithms directly onto hardware. Applications abound in many directions, including data centers, IoT, AI, image processing and space exploration. The increasing success of FPGAs is largely due to an improved toolchain with solid high-level synthesis support as well as a better integration with processor and memory systems. On the other hand, long compile times and complex design exploration remain areas for improvement. In this paper we address the evolution of FPGAs towards advanced multi-functional accelerators, discuss different programming models and their HLS language implementations, as well as high-performance tuning of FPGAs integrated into a heterogeneous platform. We pinpoint fallacies and pitfalls, and identify opportunities for language enhancements and architectural refinements

Anaesthesia Fluid Detection in 3D Contrast Enhanced Ultrasound Image

Ultrasound medical image has disadvantage on displaying anaesthesia fluid due to its low intensity. Using contrast agent to enhance brightness of fluid area makes it possible to extract fluid area from acquired 3D image. This paper proposes an easy to implement approach to detect anaesthesia fluid. The approach will slice 3D image into arrays of 2D image, remove low intensities area from image, reconstruct fluid area to its original size, and combine 2D fluid area images into 3D visualization. The purpose of this paper is to help anaesthetist to confirm whether the operation is success and for further studying on how anaesthesia fluid spread

Formal Representation of the SS-DB Benchmark and Experimental Evaluation in EXTASCID

Evaluating the performance of scientific data processing systems is a difficult task considering the plethora of application-specific solutions available in this landscape and the lack of a generally-accepted benchmark. The dual structure of scientific data coupled with the complex nature of processing complicate the evaluation procedure further. SS-DB is the first attempt to define a general benchmark for complex scientific processing over raw and derived data. It fails to draw sufficient attention though because of the ambiguous plain language specification and the extraordinary SciDB results. In this paper, we remedy the shortcomings of the original SS-DB specification by providing a formal representation in terms of ArrayQL algebra operators and ArrayQL/SciQL constructs. These are the first formal representations of the SS-DB benchmark. Starting from the formal representation, we give a reference implementation and present benchmark results in EXTASCID, a novel system for scientific data processing. EXTASCID is complete in providing native support both for array and relational data and extensible in executing any user code inside the system by the means of a configurable metaoperator. These features result in an order of magnitude improvement over SciDB at data loading, extracting derived data, and operations over derived data.Comment: 32 pages, 3 figure

Probing terahertz surface plasmon waves in graphene structures

Epitaxial graphene mesas and ribbons are investigated using terahertz (THz) nearfield microscopy to probe surface plasmon excitation and THz transmission properties on the sub-wavelength scale. The THz near-field images show variation of graphene properties on a scale smaller than the wavelength, and excitation of THz surface waves occurring at graphene edges, similar to that observed at metallic edges. The Fresnel reflection at the substrate SiC/air interface is also found to be altered by the presence of graphene ribbon arrays, leading to either reduced or enhanced transmission of the THz wave depending on the wave polarization and the ribbon width.Comment: accepted for publication in Applied Physics Lette

Optical control of photon tunneling through an array of nanometer scale cylindrical channels

We report first observation of photon tunneling gated by light at a different wavelength in an artificially created array of nanometer scale cylindrical channels in a thick gold film. Polarization properties of gated light provide strong proof of the enhanced nonlinear optical mixing in nanometric channels involved in the process. This suggests the possibility of building a new class of "gated" photon tunneling devices for massive parallel all-optical signal and image processing.Comment: 4 pages, 4 figure

A Survey on Array Storage, Query Languages, and Systems

Since scientific investigation is one of the most important providers of massive amounts of ordered data, there is a renewed interest in array data processing in the context of Big Data. To the best of our knowledge, a unified resource that summarizes and analyzes array processing research over its long existence is currently missing. In this survey, we provide a guide for past, present, and future research in array processing. The survey is organized along three main topics. Array storage discusses all the aspects related to array partitioning into chunks. The identification of a reduced set of array operators to form the foundation for an array query language is analyzed across multiple such proposals. Lastly, we survey real systems for array processing. The result is a thorough survey on array data storage and processing that should be consulted by anyone interested in this research topic, independent of experience level. The survey is not complete though. We greatly appreciate pointers towards any work we might have forgotten to mention.Comment: 44 page

Single Color Centers Implanted in Diamond Nanostructures

The development of materials processing techniques for optical diamond nanostructures containing a single color center is an important problem in quantum science and technology. In this work, we present the combination of ion implantation and top-down diamond nanofabrication in two scenarios: diamond nanopillars and diamond nanowires. The first device consists of a 'shallow' implant (~20nm) to generate Nitrogen-vacancy (NV) color centers near the top surface of the diamond crystal. Individual NV centers are then isolated mechanically by dry etching a regular array of nanopillars in the diamond surface. Photon anti-bunching measurements indicate that a high yield (>10%) of the devices contain a single NV center. The second device demonstrates 'deep' (~1\mu m) implantation of individual NV centers into pre-fabricated diamond nanowire. The high single photon flux of the nanowire geometry, combined with the low background fluorescence of the ultrapure diamond, allows us to sustain strong photon anti-bunching even at high pump powers.Comment: 20 pages, 7 figure